Download powerpoint

Virus evolution
Review Zhao (2007) Philosophical Transactions of the
Royal Society B 362: 1063 -81 (on VITAL)
SARS is caused by a coronavirus
Infected individuals can be recognised and isolated before
they became infectious
SCoV phylogeny
Beijing
Guangdong
Hong Kong
Singapore
Canada
Hong Kong
SCoV epidemiology
SARS epidemic
Caused by coronavirus (SCoV).
Animal to human transfer?
SCoV structure
SCoV phylogeny
Guan et al (2003) Science 302:276-278
Palm civet
…But 2005 study
•
•
•
•
Li et al 2005 Science 310; 676-79
Farmed civets not widely infected
If infected show overt signs
Wider sampling showed bats infected with
nearly identical virus to SARS.
• Greater genetic diversity of this virus in bats
supports bats as natural reservoir
SARS epidemiology & molecular phylogeny
Science 303: 1666 - 1669
DOI: 10.1126/science.1092002
SARS epidemiology & molecular phylogeny
SARS epidemiology & molecular phylogeny
SARS spread
Hong Kong
Late
Singapore
Science (2004)
303: 1666-69
Middle
Guangdong
Early
dN vs. dS
DNA
CCA
CCG
CGA
protein
Pro
Pro
Arg
ancestral
synonymous nonsubstitution synonymous
substitution
dN vs. dS
• No selection dN = dS
• Purifying selection dN < dS
• Positive selection dN > dS
(dN, non-synonymous substitution;
dS, synonymous substitution)
Adaptive evolution during SARS epidemic?
Synonymous substitutions
accumulate fairly constantly
over time
Adaptive evolution during SARS epidemic?
Proteins Epidemic dN/dS (± s.e.)
phase
early
1.248 (±
0.081)
middle
0.410 (±
Spike
0.087)
late
0.219 (±
0.043)
early
0.562 (±
0.145)
middle
0.315 (±
Orf1b
0.108)
late
0.344 (±
0.048)
H1
P-value
early > middle 2.3 x 10-7
middle > late 0.034
early > late
0.091
Middle phase Spike protein (SBJ01) made progressively more
‘civet-like’ (from Zhao review)
http://pathogenomics.bham.ac.uk/blog/
MERS-CoV
Source, BBC News website
http://www.hpa.org.uk/webw/HPAweb&H
PAwebStandard/HPAweb_C/13171362464
79
accessed 22/2/13
avma.org